Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean Dominique Boeufa,1, Bethanie R. Edwardsa,1,2, John M. Eppleya,1, Sarah K. Hub,3, Kirsten E. Poffa, Anna E. Romanoa, David A. Caronb, David M. Karla, and Edward F. DeLonga,4 aDaniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822; and bDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089 Contributed by Edward F. DeLong, April 22, 2019 (sent for review February 21, 2019; reviewed by Eric E. Allen and Peter R. Girguis) Sinking particles are a critical conduit for the export of organic sample both suspended as well as slowly sinking POM. Because material from surface waters to the deep ocean. Despite their filtration methods can be biased by the volume of water filtered importance in oceanic carbon cycling and export, little is known (21), also collect suspended particles, and may under-sample about the biotic composition, origins, and variability of sinking larger, more rapidly sinking particles, it remains unclear how well particles reaching abyssal depths. Here, we analyzed particle- they represent microbial communities on sinking POM in the associated nucleic acids captured and preserved in sediment traps deep sea. Sediment-trap sampling approaches have the potential at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9- to overcome some of these difficulties because they selectively month time-series, Bacteria dominated both the rRNA-gene and capture sinking particles. rRNA pools, followed by eukaryotes (protists and animals) and trace The Hawaii Ocean Time-series Station ALOHA is an open- amounts of Archaea. Deep-sea piezophile-like Gammaproteobacte- ocean study site (22° 45′ N, 158° W) where long-term ecosystem > ria, along with Epsilonproteobacteria, comprised 80% of the bac- variability and associated microbial biogeochemistry have been terial inventory. Protists (mostly Rhizaria, Syndinales, and ciliates) intensively monitored in the North Pacific Subtropical Gyre for and metazoa (predominantly pelagic mollusks and cnidarians) were over 30 y (22). One component of this effort has included time-series the most common sinking particle-associated eukaryotes. Some near- surface water-derived eukaryotes, especially Foraminifera, Radiolaria, Significance and pteropods, varied greatly in their abundance patterns, presum- ably due to sporadic export events. The dominance of piezophile-like Gammaproteobacteria and Epsilonproteobacteria, along with the Sinking particles composed of both organic and inorganic ma- prevalence of their nitrogen cycling-associated gene transcripts, sug- terial feed the deep-sea ecosystem and contribute centrally to gested a central role for these bacteria in the mineralization and bio- ocean carbon sequestration. Despite their importance, little is geochemical transformation of sinking particulate organic matter in known about the biological composition of sinking particles the deep ocean. Our data also reflected several different modes of reaching the deep sea. Time-series analyses of sinking particles particle export dynamics, including summer export, more stochastic unexpectedly revealed bacterial assemblages that were simple inputs from the upper water column by protists and pteropods, and and homogeneous over time. Particle-associated eukaryote as- contributions from sinking mid- and deep-water organisms. In total, semblages, however, were more variable and complex. Several our observations revealed the variable and heterogeneous biological modes of export were observed, including summer inputs from origins and microbial activities of sinking particles that connect their the surface, more stochastic export of surface-derived protists downward transport, transformation, and degradation to deep-sea and animals, and contributions from midwater animals and biogeochemical processes. deep-sea bacteria. In summary, sinking particles exhibited tem- porally variable, heterogeneous biological sources and activities deep sea | marine microbes | particulate organic matter | that reflected their important roles in the downward transport marine carbon cycle | piezophile and transformation of organic matter in the deep sea. Author contributions: D.M.K. and E.F.D. designed research; D.B., B.R.E., J.M.E., S.K.H., hotosynthetic primary production in marine surface waters is K.E.P., A.E.R., D.A.C., and E.F.D. performed research; J.M.E. contributed new reagents/ Pdelivered to the abyss via sinking particles, fueling food webs, analytic tools; D.B., B.R.E., J.M.E., S.K.H., K.E.P., A.E.R., D.A.C., D.M.K., and E.F.D. analyzed and biogeochemical cycles in the deep ocean (1). Sinking par- data; and E.F.D. wrote the paper with D.B., B.R.E., S.K.H., D.A.C., and D.M.K. ticulate organic matter (POM) is the primary conduit for con- Reviewers: E.E.A., University of California, San Diego; and P.R.G., Harvard University. necting surface water productivity to the deep sea, with lesser The authors declare no conflict of interest. contributions from downward diffusion of dissolved organic This open access article is distributed under Creative Commons Attribution-NonCommercial- carbon and macrozooplankton vertical migration (2). The solar NoDerivatives License 4.0 (CC BY-NC-ND). energy-driven “biological pump” also contributes to the export Data deposition: The metagenome and metatranscriptome and prokaryote small subunit and sequestration of carbon dioxide to the deep sea. ribosomal RNA amplicon sequence datasets reported in this study have been deposited in the NCBI Sequence Read Archive (project no. PRJNA482655); the eukaryotic small subunit Microbes associated with sinking particles may influence car- ribosomal RNA amplicon sequences have been deposited in the NCBI Sequence Read bon export efficiency by facilitating aggregation/disaggregation Archive (project no. PRJNA393049). activities, POM degradation, and trophic transfer of POM- 1D.B., B.R.E., and J.M.E. contributed equally to this work. – associated organic carbon and energy (3 6). The taxonomic com- 2Present address: Department of Earth and Planetary Science, University of California, position of marine particle-associated microbes has been examined Berkeley, CA 94720. on a variety of different particle types using different methodologies 3Present address: Marine Chemistry & Geochemistry Department, Woods Hole Oceano- (7–16). Recent studies have focused on near-surface water samples graphic Institution, Woods Hole, MA 02543-1050. that are derived from single time points, and most have used 4To whom correspondence may be addressed. Email: [email protected]. filter fractionation techniques to capture particle-associated mi- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. crobes. A few deep-sea studies have examined microbial diversity 1073/pnas.1903080116/-/DCSupplemental. on filter-fractionated deep-sea particles as well (17–20), that Published online May 24, 2019. 11824–11832 | PNAS | June 11, 2019 | vol. 116 | no. 24 www.pnas.org/cgi/doi/10.1073/pnas.1903080116 Downloaded by guest on October 6, 2021 studies of particle export to the deep sea (at 2,800 m and followed by 40% Eukaryote and 0.6% Archaea rRNA genes (Fig. 4,000 m) for over 25 y (23). In combination with surface primary 1 and Table 1). In the RNA-based metatranscriptome libraries, production and euphotic zone export measurements, these ef- 83.9% of the annotated rRNAs originated from Bacteria, followed forts have revealed the variability of organic matter export to the by 16% Eukaryote and 0.1% Archaea rRNAs. deep sea at Station ALOHA, and its quantitative biogeochemical Across the 9-mo sampling period, the sinking particle-associated significance. In particular, strong seasonality in particulate or- microbial assemblage was dominated in both the metagenome ganic carbon (POC) flux to the seafloor was observed with values and the metatranscriptome by two main bacterial groups: the − − − − ranging from 98.6 μmol C·m 2·d 1 in winter, to 282.7 μmol C·m 2·d 1 gammaproteobacterial order Alteromonadales and the epsilon- in the summer (23). This approximately threefold increase in in proteobacterial order Campylobacterales (Fig. 1 and Table 1). summertime particle flux, referred to as the “summer export pulse” Alteromonadales comprised 25% of SSU rRNA genes in DNA (SEP), is believed to be fueled by blooms associated with sym- and 26.9% SSU rRNAs in RNA. Campylobacterales represented biotic nitrogen-fixing cyanobacteria-diatom phytoplankton as- 19.3% and 40.5% of particle-associated SSU rRNA genes and semblages (23). However, for unknown reasons, in some years SSU rRNAs, respectively (Table 1). Together, these two bacte- (including the 2014 samples reported here) the average summer rial groups represented 45% of all annotated SSU RNA genes in and winter particle fluxes are not significantly different (23). the metagenomes, and 67% SSU rRNAs of all annotated rRNAs Beyond these details, and despite the extensive and informative in the metatranscriptomes. This trend was consistent within in- biogeochemical time-series datasets available, little is known dividual samples across the entire 2014 time series in the meta- about the biological origins and processes occurring on sinking genome, metatranscriptome (Fig. 1), and PCR-based rRNA POM reaching abyssal depths at Station ALOHA. amplicon libraries (SI Appendix,Fig.S2). To better